Many studies have shown that zooplankton patches and the physical and biological processes that create them operate over a continuum of spatial and temporal scales. In tropical coastal areas, impacts of spatial scales on zooplankton communities and their relationships to the environment have not been previously considered. We examined the processes constraining the zooplankton communities in a coastal reef lagoon, in order to understand the factors that contribute to the generation of its multiscale spatial structure. To analyze zooplankton spatial structure, we used the principal coordinates of neighbor matrices. The resulting scalogram showed that zooplankton patches, in terms of biomass and abundance, changed along a spatial scale continuum. The analysis of the various physical and biological factors that explain this variability was conducted using canonical analyses and partial Mantel tests. The physical and biological processes including local hydrodynamics, phytoplankton distribution and zooplankton behavior, generate zooplankton spatial patterns. The type and the effects of these processes are dependent on spatial scale. This work helps to explain why zooplankton community responses, in term of biomass and abundance, change along the scale continuum.